Contacts of the strand formed by residues 106 - 113 (chain D) in PDB entry 3AQQ


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLU 106 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  TYR*     4.0     1.4    -      -       -      -
     83B  ASP*     2.4    35.3    -      -       -      +
     64D  LYS*     3.0    35.5    +      -       +      +
     65D  GLY      3.3    15.9    -      -       -      +
     66D  VAL*     4.5    10.3    -      -       +      +
    104D  GLY      3.3     5.0    +      -       -      +
    105D  ASP*     1.3    70.5    -      -       -      +
    107D  VAL*     1.3    63.8    +      -       -      +
    128D  ILE*     3.5     2.1    -      -       -      -
    129D  THR*     2.8    30.1    +      -       -      +
    130D  HIS*     2.8    45.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 107 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64D  LYS*     3.3     5.1    -      -       -      +
     65D  GLY*     2.7    57.8    +      -       -      +
     66D  VAL*     3.9     3.8    -      -       -      +
     67D  CYS*     4.4     6.1    -      -       +      +
     79D  ILE*     3.8    27.4    -      -       +      -
    101D  PRO*     6.2     1.6    -      -       +      -
    105D  ASP*     3.9    13.5    -      -       +      +
    106D  GLU*     1.3    80.9    -      -       -      +
    108D  THR*     1.3    66.5    +      -       -      +
    109D  TYR*     3.9     6.2    -      -       +      -
    126D  VAL*     4.4     9.9    -      -       +      -
    127D  VAL      3.0    15.0    -      -       -      +
    128D  ILE*     4.0    16.2    -      -       +      -
    129D  THR*     4.2     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 108 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  PRO*     3.7    21.1    -      -       +      -
     63B  TYR*     3.0    28.5    -      -       -      +
     58C  SER*     4.2     6.8    +      -       -      -
     59C  GLN*     4.9     7.6    +      -       -      +
     62D  VAL*     3.9    11.4    -      -       +      -
     63D  TYR      3.1     5.6    -      -       -      +
     64D  LYS*     4.7     1.1    -      -       +      -
    107D  VAL*     1.3    76.2    -      -       -      +
    109D  TYR*     1.3    64.8    +      -       -      +
    125D  GLU      4.3     0.9    -      -       -      -
    126D  VAL*     3.5     1.9    -      -       -      +
    127D  VAL*     2.9    51.0    +      -       -      +
    129D  THR*     3.4    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 109 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62D  VAL*     3.7     4.1    -      -       -      +
     63D  TYR*     2.9    48.7    +      -       +      +
     64D  LYS      3.3    30.7    +      -       -      -
     65D  GLY      3.9     1.1    -      -       -      -
     79D  ILE*     4.0    17.9    -      -       +      -
     81D  PRO*     3.8    17.8    -      -       -      +
     88D  ILE*     4.2     8.6    -      -       +      +
    107D  VAL*     3.9    12.3    -      -       +      -
    108D  THR*     1.3    81.7    -      -       -      +
    110D  LYS*     1.3    75.1    +      -       -      +
    111D  MET*     3.7    36.8    -      -       +      +
    123D  ALA*     3.9    12.3    -      -       +      -
    124D  VAL      3.7     8.5    -      -       -      +
    125D  GLU      3.6     9.2    -      -       -      -
    126D  VAL*     3.9    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 110 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110C  LYS*     4.2    15.6    -      -       -      +
    125C  GLU*     4.6     0.6    +      -       -      -
     57D  ALA      3.2    26.2    -      -       -      +
     58D  SER*     3.2    28.3    -      -       -      +
     60D  GLY      4.2     7.2    -      -       -      +
     61D  PRO      3.8    15.3    -      -       -      +
     62D  VAL*     4.3    19.4    -      -       +      +
    109D  TYR*     1.3    85.5    -      -       -      +
    111D  MET*     1.3    62.4    +      -       -      +
    123D  ALA*     3.5     0.2    -      -       -      -
    124D  VAL*     2.9    41.4    +      -       +      +
    125D  GLU*     2.9    32.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 111 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57D  ALA*     3.5    24.3    +      -       -      +
     61D  PRO*     4.5     4.4    +      -       -      +
     63D  TYR*     4.0    29.1    -      -       +      -
     81D  PRO*     5.1     5.6    -      -       +      -
     83D  ASP*     5.8     2.5    -      -       -      +
     88D  ILE*     3.6    25.8    -      -       +      -
    109D  TYR*     3.7    35.4    -      -       +      +
    110D  LYS*     1.3    74.8    -      -       -      +
    112D  CYS*     1.3    63.4    +      -       -      +
    121D  LEU*     3.1    32.1    -      -       +      -
    122D  GLN      3.4    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 112 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  ARG*     3.7    32.1    -      -       -      -
     53D  ALA*     4.4    13.2    -      -       -      -
     57D  ALA*     4.0    13.2    -      -       -      +
    111D  MET*     1.3    77.2    -      -       -      +
    113D  SER*     1.3    67.7    +      -       -      +
    121D  LEU*     3.2    10.1    -      -       -      +
    122D  GLN*     2.6    46.5    +      -       +      +
    124D  VAL*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 113 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  ALA*     5.6     2.9    -      -       -      +
     56D  ARG*     6.1     2.5    -      -       -      -
    112D  CYS*     1.3    85.5    -      -       -      +
    114D  ILE*     1.3    60.8    +      -       -      +
    115D  PRO*     3.4    11.6    -      -       -      +
    118D  ASN*     3.1    35.7    -      -       -      +
    119D  GLU      3.7     5.2    +      -       -      -
    120D  LYS      3.1    17.2    +      -       -      -
    121D  LEU*     3.8     8.4    -      -       -      +
    122D  GLN*     5.3     1.2    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il